Merge branch 'development' of github.com:opentox/install into development

9 files changed, 40 insertions, 492 deletions

diff --git a/4store-install b/4store-install
index 8b78d41..3e310ed 100755
--- a/4store-install
+++ b/4store-install
@@ -10,12 +10,13 @@ DIR=`pwd`
 SELF=$(basename $0 -install)
 check_log $SELF
 [ "`id -u`" = "0" ] && echo "This script must not be run as root" 1>&2 && exit 1
-check_utils "git make"
+check_utils "git make tar wget"
 
 # Build
 cd $OT_PREFIX/tmp/
 ([ -d $SELF ] && cd $SELF && cmd="$GIT pull" && run_cmd "$cmd" "Git pull") || (cmd="$GIT clone https://github.com/garlik/$SELF" && run_cmd "$cmd" "Git clone")
 cd $SELF
+cmd="$GIT checkout -b ist c3d8593c39dc04a39e272f729e486c1576f6aeba" && run_cmd "$cmd" "checkout to particular commit"
 cmd="./autogen.sh" && run_cmd "$cmd" "Autogen"
 export FST=$OT_PREFIX/4S
 cmd="./configure --prefix=$FST --exec-prefix=$FST --with-storage-path=$FST/var/lib --with-config-file=$FST/$SELF.conf -with-http-log=$FST/log CFLAGS=-O2 CPPFLAGS=-O3" && run_cmd "$cmd" "Configure"
@@ -25,7 +26,7 @@ cmd="make install" && run_cmd "$cmd" "Make Install"
 
 # Config
 echo "if echo \"\$LD_LIBRARY_PATH\" | grep -v \"$FST/lib\">/dev/null 2>&1; then export LD_LIBRARY_PATH=\"\$LD_LIBRARY_PATH:$FST/lib\"; fi" >> "$FST_CONF"
-if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "", :password => "" }' >> $OT_DEFAULT_CONF; fi
+if ! cat "$OT_DEFAULT_CONF" | grep "four_store">/dev/null 2>&1; then echo '$four_store = { :uri => "http://localhost:9088", :user => "user", :password => "pw" }' >> $OT_DEFAULT_CONF; fi
 
 echo "$SELF configuration stored in '$FST_CONF'."
 if ! grep "$FST_CONF" $OT_UI_CONF >/dev/null 2>&1; then
diff --git a/base-install b/base-install
index 444d7f9..44abffd 100755
--- a/base-install
+++ b/base-install
@@ -28,6 +28,7 @@ if ! cat "/etc/apt/sources.list" | grep "$REDLAND_DEB">/dev/null 2>&1; then
 fi
 
 sudo $APTITUDE update -y >/dev/null 2>&1
+sudo $APTITUDE upgrade -y >/dev/null 2>&1
 
 DISTRIB_INFO=$(cat /proc/version)
 
@@ -37,6 +38,7 @@ case "$DISTRIB_INFO" in
   *) PACK_LIST="debian.list";;
 esac
 
+sudo $APTITUDE update -y >/dev/null 2>&1
 sudo $DPKG --set-selections < "$PACK_LIST"
 sudo $APT_GET -y --force-yes -u dselect-upgrade
 
@@ -44,6 +46,8 @@ if [ ! -f $JAVA_CONF ]; then
 
   if [ ! -d "$OT_JAVA_HOME" ]; then
     echo "Directory '$OT_JAVA_HOME' does not exist! Aborting..."
+    echo "Please check if openjdk-6-jdk has been installed properly."
+    echo "You may need to set the OT_JAVA_HOME variable in config.sh to the correct path on your system."
     exit 1
   fi
 
diff --git a/config.sh b/config.sh
index 16c6ad8..9cdbca7 100755
--- a/config.sh
+++ b/config.sh
@@ -18,9 +18,16 @@ OT_JAVA_HOME="/usr/lib/jvm/java-6-openjdk"
 OB_NUM_VER="2.3.1"
 RAPTOR2_NUM_VER="2.0.8"
 RASQAL_NUM_VER="0.9.29"
+REDIS_NUM_VER="2.4.4"
 RUBY_NUM_VER="1.9.3-p194"
+FOUR_STORE_VER="4store-v1.1.5"
+REDIS_URL="http://redis.googlecode.com/files"
 REDLAND_DWL="http://download.librdf.org"
 REDLAND_APT_KEY="http://purl.org/net/dajobe/gnupg.asc"
+FOUR_STORE_URL="http://4store.org/download"
+
+# 4) Server settings.
+OHM_PORT="6379" # set to port (no colon)
 
 # Done.
 
@@ -31,6 +38,7 @@ OB_CONF="$HOME/.opentox/OB.sh"
 R_CONF="$HOME/.opentox/R.sh"
 RAPTOR2_CONF="$HOME/.opentox/RAPTOR2.sh"
 RASQAL_CONF="$HOME/.opentox/RASQAL.sh"
+REDIS_CONF="$HOME/.opentox/REDIS.sh"
 OT_UI_CONF="$HOME/.opentox/opentox-ui.sh"
 OT_TOOLS_CONF="$HOME/.opentox/ot-tools.sh"
 OT_DEFAULT_CONF="$HOME/.opentox/config/default.rb"
@@ -38,10 +46,15 @@ OT_DEFAULT_CONF="$HOME/.opentox/config/default.rb"
 OB_VER="openbabel-$OB_NUM_VER"
 RAPTOR2_VER="raptor2-$RAPTOR2_NUM_VER"
 RASQAL_VER="rasqal-$RASQAL_NUM_VER"
+REDIS_VER="redis-$REDIS_NUM_VER"
 OB_DEST="$OT_PREFIX/$OB_VER"
 OB_DEST_BINDINGS="$OT_PREFIX/openbabel-ruby-install"
 R_DEST="$OT_PREFIX/r-packages"
 RUBY_DWL="http://ftp.ruby-lang.org/pub/ruby/1.9"
 RAPTOR2_DWL="$REDLAND_DWL/source/$RAPTOR2_VER.tar.gz"
 RASQAL_DWL="$REDLAND_DWL/source/$RASQAL_VER.tar.gz"
+REDIS_DWL="$REDIS_URL/$REDIS_VER.tar.gz"
+REDIS_DIR="$OT_PREFIX/$REDIS_VER"
+REDIS_SERVER_CONF="$REDIS_DIR/redis.conf"
 REDLAND_DEB="$REDLAND_DWL/binaries/$OT_DIST/unstable"
+FOUR_STORE_DWL="$FOUR_STORE_URL/$FOUR_STORE_VER.tar.gz"
diff --git a/debian.list b/debian.list
index b10234d..e5af5b5 100644
--- a/debian.list
+++ b/debian.list
@@ -4,6 +4,7 @@ avahi-daemon install
 build-essential install
 cmake install
 curl install
+gnuplot install
 libavahi-glib-dev install
 libavahi-client-dev install
 libcairo2-dev install
@@ -22,3 +23,4 @@ openjdk-6-jdk install
 r-base-dev install
 r-base install
 uuid-dev install
+xsltproc install
diff --git a/install b/install
index c9663ba..1dea679 100755
--- a/install
+++ b/install
@@ -71,11 +71,8 @@ if ! grep "rbenv" $OT_UI_CONF >/dev/null 2>&1 ; then
   echo 'if ! echo "$PATH" | grep "$HOME/.rbenv/bin">/dev/null 2>&1; then export PATH="$HOME/.rbenv/bin:$PATH"; eval "$(rbenv init -)"; fi' >> $OT_UI_CONF
 fi
 
-[ -f $HOME/.opentox/config/pc_descriptors.yaml ] || (cmd="cp pc_descriptors.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Pc descriptor file")
-[ -f $HOME/.opentox/config/jl_keys.yaml ] || (cmd="cp jl_keys.yaml $HOME/.opentox/config/" && run_cmd "$cmd" "Joelib keys file")
 [ -f $OT_TOOLS_CONF ] || (cmd="cp ot-tools-user.sh $OT_TOOLS_CONF" && run_cmd "$cmd" "ot-tools.sh => $HOME/.opentox")
 
-
 # Install global ruby version
 . ./utils.sh
 install_ruby global
diff --git a/jl_keys.yaml b/jl_keys.yaml
deleted file mode 100644
index 22f26ae..0000000
--- a/jl_keys.yaml
+++ /dev/null
@@ -1,38 +0,0 @@
-[
-  "joelib2.feature.types.FractionRotatableBonds",
-  "joelib2.feature.types.GeometricalDiameter",
-  "joelib2.feature.types.GeometricalRadius",
-  "joelib2.feature.types.GeometricalShapeCoefficient",
-  "joelib2.feature.types.GraphShapeCoefficient",
-  "joelib2.feature.types.KierShape1",
-  "joelib2.feature.types.KierShape2",
-  "joelib2.feature.types.KierShape3",
-  "joelib2.feature.types.LogP",
-  "joelib2.feature.types.MolarRefractivity",
-  "joelib2.feature.types.MolecularWeight",
-  "joelib2.feature.types.PolarSurfaceArea",
-  "joelib2.feature.types.FractionRotatableBonds",
-  "joelib2.feature.types.RotatableBonds",
-  "joelib2.feature.types.TopologicalDiameter",
-  "joelib2.feature.types.TopologicalRadius",
-  "joelib2.feature.types.ZagrebIndex1",
-  "joelib2.feature.types.count.AcidicGroups",
-  "joelib2.feature.types.count.AliphaticOHGroups",
-  "joelib2.feature.types.count.AromaticBonds",
-  "joelib2.feature.types.count.AromaticOHGroups",
-  "joelib2.feature.types.count.BasicGroups",
-  "joelib2.feature.types.count.HBA1",
-  "joelib2.feature.types.count.HBA2",
-  "joelib2.feature.types.count.HBD1",
-  "joelib2.feature.types.count.HBD2",
-  "joelib2.feature.types.count.HeavyBonds",
-  "joelib2.feature.types.count.HeteroCycles",
-  "joelib2.feature.types.count.HydrophobicGroups",
-  "joelib2.feature.types.count.NO2Groups",
-  "joelib2.feature.types.count.NumberOfAtoms",
-  "joelib2.feature.types.count.NumberOfBonds",
-  "joelib2.feature.types.count.NumberOfHal",
-  "joelib2.feature.types.count.OSOGroups",
-  "joelib2.feature.types.count.SO2Groups",
-  "joelib2.feature.types.count.OSOGroups"
-]
diff --git a/ot-tools-user.sh b/ot-tools-user.sh
index bb036ef..47f0f66 100644
--- a/ot-tools-user.sh
+++ b/ot-tools-user.sh
@@ -27,9 +27,9 @@ start_unicorn() {
 # @example start_unicorn algorithm 8081
 start_4s() {
   nice bash -c "nohup $OT_PREFIX/4S/bin/4s-backend $1 >/dev/null 2>&1 &";
-  sleep 0.5;
+  sleep 2;
   nice bash -c "nohup $OT_PREFIX/4S/bin/4s-httpd -H localhost -p $2 -s -1 $1 >/dev/null 2>&1 &"; #-D for testing        
-  sleep 0.5;
+  sleep 1;
 
 }
 
@@ -72,8 +72,8 @@ otstart() {
     "feature")    start_unicorn $1 8084;;
     "model")      start_unicorn $1 8085;;
     "task")       start_unicorn $1 8086;;
-    "validation") #start_unicorn $1 8087;;
-                  echo "$1 not available yet.";;
+    "validation") start_unicorn $1 8087;
+                  nice bash -c "nohup redis-server $OT_PREFIX/validation/redis-*/redis.conf >/dev/null 2>&1 &";;
     "4store")     start_4s opentox 9088; 
                   if ! pgrep -u $USER 4s-backend>/dev/null 2>&1; then echo "Failed to start 4s-backend."; fi
                   if ! pgrep -u $USER 4s-httpd>/dev/null 2>&1; then echo "Failed to start 4s-httpd."; fi;;
@@ -83,8 +83,8 @@ otstart() {
                   otstart dataset;
                   otstart feature;
                   otstart model;
-                  otstart task;;
-                  #otstart validation;;
+                  otstart task;
+                  otstart validation;;
     *)            echo "One argument required: [service_name] or 'all'";
                   echo "usage: otstart [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
                   return 1;;
@@ -132,9 +132,8 @@ otreload() {
                   check_service "model";;
     "task")       reload_unicorn 8086;
                   check_service "task";;
-    "validation") #reload_unicorn 8087;;
-                  #check_service "validation";
-                  echo "$1 not available yet.";;
+    "validation") reload_unicorn 8087;
+                  check_service "validation";;
     "4store")     #killall 4s-httpd >/dev/null 2>&1;
                   #killall 4s-backend >/dev/null 2>&1;
                   #check_service "four_store";;
@@ -144,8 +143,8 @@ otreload() {
                   otreload dataset;
                   otreload feature;
                   otreload model;
-                  otreload task;;
-                  #otrelaod validation;
+                  otreload task;
+                  otrelaod validation;;
                   #otreload 4store;;
     *)            echo "One argument required: [service_name] or 'all'";
                   echo "usage: otreload [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
@@ -176,8 +175,8 @@ otkill() {
     "feature")    kill_unicorn 8084;;
     "model")      kill_unicorn 8085;;
     "task")       kill_unicorn 8086;;
-    "validation") #kill_unicorn 8087;;
-                  echo "$1 not available yet.";;
+    "validation") kill_unicorn 8087;
+                  bash -c "redis-cli -p $OHM_PORT shutdown >/dev/null 2>&1";;
     "4store")     killall 4s-httpd >/dev/null 2>&1;
                   killall 4s-backend >/dev/null 2>&1;;
     "all")        otkill algorithm;
@@ -186,7 +185,7 @@ otkill() {
                   otkill feature;
                   otkill model;
                   otkill task;
-                  #otkill validation;
+                  otkill validation;
                   otkill 4store;;
     *)            echo "One argument required: [service_name] or 'all'";
                   echo "usage: otkill [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
@@ -265,8 +264,7 @@ otcheck() {
     "feature")    check_service "feature";;
     "model")      check_service "model";;
     "task")       check_service "task";;
-    "validation") #check_service "validation";;
-                  echo "$1 not available yet.";;
+    "validation") check_service "validation";;
     "4store")     check_service "four_store";; 
     "all")        otcheck "algorithm";
                   otcheck "compound";
@@ -274,7 +272,7 @@ otcheck() {
                   otcheck "feature";
                   otcheck "model";
                   otcheck "task";
-                  #otcheck "validation";
+                  otcheck "validation";
                   otcheck 4store;;
     *)            echo "One argument required: [service_name] or 'all'";
                   echo "usage: otcheck [all|algorithm|compound|dataset|feature|model|task|validation|4store]";
diff --git a/pc_descriptors.yaml b/pc_descriptors.yaml
deleted file mode 100644
index ba32800..0000000
--- a/pc_descriptors.yaml
+++ /dev/null
@@ -1,432 +0,0 @@
---- 
-
-# cdk
-
-LengthOverBreadthDescriptor: 
-  :pc_type: "geometrical"
-  :lib: "cdk"
-  :name: "Length Over Breadth"
-
-KierHallSmartsDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Kier & Hall SMARTS"
-
-FragmentComplexityDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Fragment Complexity"
-
-APolDescriptor:
-  :pc_type: "electronic"
-  :lib: "cdk"
-  :name: "Atomic Polarizabilities"
-
-LargestChainDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Largest Chain"
-
-ChiPathDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Chi Path Indices"
-
-PetitjeanNumberDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Petitjean Number"
-
-LongestAliphaticChainDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Longest Aliphatic Chain"
-
-KappaShapeIndicesDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Kier and Hall kappa molecular shape indices"
-
-AromaticBondsCountDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Aromatic Bonds Count"
-
-CPSADescriptor:
-  :pc_type: "cpsa"
-  :lib: "cdk"
-  :name: "Charged Partial Surface Areas"
-
-VAdjMaDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Vertex adjacency information magnitude"
-
-AutocorrelationDescriptorMass:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Moreau-Broto Autocorrelation (mass) descriptors"
-
-RuleOfFiveDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Lipinski's Rule of Five"
-
-GravitationalIndexDescriptor:
-  :pc_type: "geometrical"
-  :lib: "cdk"
-  :name: "Gravitational Index"
-
-WienerNumbersDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Wiener Numbers"
-
-ChiPathClusterDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Chi Path-Cluster Indices"
-
-AtomCountDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Atoms Count"
-
-MomentOfInertiaDescriptor:
-  :pc_type: "geometrical"
-  :lib: "cdk"
-  :name: "Moments of Inertia"
-
-CarbonTypesDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Carbon Types"
-
-AutocorrelationDescriptorPolarizability:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Moreau-Broto Autocorrelation (polarizability) descriptors"
-
-EccentricConnectivityIndexDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Eccentric Connectivity Index"
-
-BCUTDescriptor:
-  :pc_type: "hybrid"
-  :lib: "cdk"
-  :name: "BCUT"
-
-AromaticAtomsCountDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Aromatic Atoms Count"
-
-WHIMDescriptor:
-  :pc_type: "hybrid"
-  :lib: "cdk"
-  :name: "WHIM"
-
-ALOGPDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "ALogP"
-
-XLogPDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "XLogP"
-
-PetitjeanShapeIndexDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Petitjean Number"
-
-MDEDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Molecular Distance Edge"
-
-ChiChainDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Chi Chain Indices"
-
-BondCountDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Bonds Count"
-
-MannholdLogPDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Mannhold LogP"
-
-BPolDescriptor:
-  :pc_type: "electronic"
-  :lib: "cdk"
-  :name: "Bond Polarizabilities"
-
-AutocorrelationDescriptorCharge:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Moreau-Broto Autocorrelation (charge) descriptors"
-
-ZagrebIndexDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Zagreb Index"
-
-ChiClusterDescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Chi Cluster Indices"
-
-RotatableBondsCountDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Rotatable Bonds Count"
-
-TPSADescriptor:
-  :pc_type: "topological"
-  :lib: "cdk"
-  :name: "Topological Polar Surface Area"
-
-HBondDonorCountDescriptor:
-  :pc_type: "electronic"
-  :lib: "cdk"
-  :name: "Hydrogen Bond Donors"
-
-HBondAcceptorCountDescriptor:
-  :pc_type: "electronic"
-  :lib: "cdk"
-  :name: "Hydrogen Bond Acceptors"
-
-LargestPiSystemDescriptor:
-  :pc_type: "constitutional"
-  :lib: "cdk"
-  :name: "Largest Pi Chain"
-
-
-# joelib
-
-
-HBA2:
-  :pc_type: "electronic"
-  :lib: "joelib"
-  :name: "Hydrogen Bond Acceptors 2"
-MolarRefractivity:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Molar Refractivity"
-KierShape3:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Kier Shape 3"
-SO2Groups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "SO2 Groups"
-MolecularWeight:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Molecular Weight"
-LogP:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Log P"
-OSOGroups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "OSO Groups"
-AromaticOHGroups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Aromatic OH Groups"
-AromaticBonds:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Aromatic Bonds"
-AcidicGroups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Acidic Groups"
-GraphShapeCoefficient:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Graph Shape Coefficient"
-GeometricalShapeCoefficient:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Geometrical Shape Coefficient"
-ZagrebIndex1:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Zagreb Index1"
-TopologicalRadius:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Topological Radius"
-GeometricalDiameter:
-  :pc_type: "geometrical"
-  :lib: "joelib"
-  :name: "Geometrical Diameter"
-FractionRotatableBonds:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Fraction Rotatable Bonds"
-NumberOfAtoms:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Number Of Atoms"
-HeteroCycles:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Hetero Cycles"
-RotatableBonds:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Rotatable Bonds"
-BasicGroups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Basic Groups"
-TopologicalDiameter:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Topological Diameter"
-NumberOfBonds:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Number Of Bonds"
-NO2Groups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "NO2 Groups"
-HBD1:
-  :pc_type: "electronic"
-  :lib: "joelib"
-  :name: "Hydrogen Bond Donors 1"
-AliphaticOHGroups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Aliphatic OH Groups"
-HBD2:
-  :pc_type: "electronic"
-  :lib: "joelib"
-  :name: "Hydrogen Bond Donors 2"
-HydrophobicGroups:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Hydrophobic Groups"
-HeavyBonds:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Heavy Bonds"
-KierShape1:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Kier Shape1"
-NumberOfHal:
-  :pc_type: "constitutional"
-  :lib: "joelib"
-  :name: "Number Of Halogens"
-HBA1:
-  :pc_type: "electronic"
-  :lib: "joelib"
-  :name: "Hydrogen Bond Acceptors 1"
-PolarSurfaceArea:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Polar Surface Area"
-KierShape2:
-  :pc_type: "topological"
-  :lib: "joelib"
-  :name: "Kier Shape 2"
-GeometricalRadius:
-  :pc_type: "geometrical"
-  :lib: "joelib"
-  :name: "Geometrical Radius"
-
-
-# openbabel
-NumAtoms:       
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Number of atoms"
-NumBonds:       
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Number of bonds"
-NumHvyAtoms:    
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Number of heavy atoms"
-NumResidues:    
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Number of residues"
-NumRotors:      
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Number of rotatable bonds"
-GetEnergy:
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Heat of formation for this molecule (in kcal/mol)"
-GetMolWt:       
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Standard molar mass given by IUPAC atomic masses (amu)"
-GetExactMass:   
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Mass given by isotopes (or most abundant isotope if not specified)"
-GetTotalCharge: 
-  :pc_type: "topological"
-  :lib: "openbabel"
-  :name: "Total charge"
-HBA1:           
-  :pc_type: "electronic"
-  :lib: "openbabel"
-  :name: "Number of hydrogen bond acceptors 1 (JoelLib)"
-HBA2:           
-  :pc_type: "electronic"
-  :lib: "openbabel"
-  :name: "Number of hydrogen bond acceptors 2 (JoelLib)"
-HBD:            
-  :pc_type: "electronic"
-  :lib: "openbabel"
-  :name: "Number of hydrogen bond donors (JoelLib)"
-L5:             
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Lipinski rule of five"
-logP:           
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Octanol/water partition coefficient"
-MR:             
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Molar refractivity"
-MW:             
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Molecular weight"
-nF:             
-  :pc_type: "constitutional"
-  :lib: "openbabel"
-  :name: "Number of fluorine atoms"
-#nHal:           
-#  :pc_type: "constitutional"
-#  :lib: "openbabel"
-#  :name: "Number of halogen atoms"
-#spinMult:       
-#  :pc_type: "electronic"
-#  :lib: "openbabel"
-#  :name: "Total spin multiplicity"
-TPSA:           
-  :pc_type: "topological"
-  :lib: "openbabel"
-  :name: "Topological polar surface area"
diff --git a/ubuntu.list b/ubuntu.list
index 923759d..e5af5b5 100644
--- a/ubuntu.list
+++ b/ubuntu.list
@@ -4,8 +4,10 @@ avahi-daemon install
 build-essential install
 cmake install
 curl install
+gnuplot install
 libavahi-glib-dev install
 libavahi-client-dev install
+libcairo2-dev install
 libglib2.0-dev install
 libgsl0-dev install
 libopenssl-ruby install
@@ -21,3 +23,4 @@ openjdk-6-jdk install
 r-base-dev install
 r-base install
 uuid-dev install
+xsltproc install